from chandra_suli.work_within_directory import work_within_directory
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Check each candidate transient for hot pixels and '
'closest variable source')
parser.add_argument("-o", "--obsid", help="Observation ID Numbers", type=int, required=True, nargs="+")
parser.add_argument("-f", "--outfile", help="Name of output file which will contain filtered list of transients",
required=True)
parser.add_argument("-d1", "--results_path", help="Path to directory containing results from farm_step_2")
parser.add_argument("-d2", "--data_path", help="Path to directory containing data of all obsids", required=True,
type=str)
# Get the logger
logger = logging_system.get_logger(os.path.basename(sys.argv[0]))
# Get the command runner
runner = CommandRunner(logger)
args = parser.parse_args()
results_path = sanitize_filename(args.results_path)
data_path = sanitize_filename(args.data_path)
for this_obsid in args.obsid:
# Go to directory where results from farm_step2 are stored
with work_within_directory(results_path):
parser.add_argument("--evtfile",
help="Filtered CCD file",
required=True,
type=str)
parser.add_argument("--outfile",
help="Output file with events in hot pixels removed",
required=True,
type=str)
parser.add_argument("--debug",
help="Debug mode? (yes or no)",
required=False,
default='no')
# Get logger for this command
logger = logging_system.get_logger(os.path.basename(sys.argv[0]))
# Instance the command runner
runner = CommandRunner(logger)
args = parser.parse_args()
eventfile = sanitize_filename(args.evtfile)
# Open event file
fits_file = pyfits.open(eventfile, mode='update', memmap=False)
# Make sure we are dealing with only one CCD
ccds = np.unique(fits_file['EVENTS'].data.ccd_id)
from chandra_suli.run_command import CommandRunner
from chandra_suli.logging_system import get_logger
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description='Create new event files separated by CCD')
parser.add_argument('--evtfile',
help="Event file name",
type=str,
required=True)
args = parser.parse_args()
logger = get_logger("separate_CCD.py")
runner = CommandRunner(logger)
print "Separating by CCD..."
for ccd_id in range(10):
ccd_file = "ccd_%s_%s" % (ccd_id, os.path.basename(args.evtfile))
cmd_line = "dmcopy %s[EVENTS][ccd_id=%s] %s clobber=yes" % (
args.evtfile, ccd_id, ccd_file)
runner.run(cmd_line)
# check if certain CCD files are empty and then delete them if so
import fnmatch
import os
import shutil
import yaml
from chandra_suli.logging_system import get_logger
from chandra_suli.sanitize_filename import sanitize_filename
from chandra_suli.work_within_directory import work_within_directory
logger = get_logger("DataPackage")
_index_file = "index.yml"
def _check_directory(directory):
sanitized_directory = sanitize_filename(directory)
assert os.path.exists(sanitized_directory), "Directory %s does not exists" % sanitized_directory
assert os.path.isdir(sanitized_directory), "The file %s is not a directory" % sanitized_directory
return sanitized_directory
class File(object):
def __init__(self, filename, description):
self._filename = sanitize_filename(filename)
self._description = description
assert os.path.exists(self._filename), "Something went wrong when creating File instance. " \
type=str,
required=True)
parser.add_argument("--debug",
help="Debug mode (yes or no)",
type=bool,
required=False,
default=False)
# assumption = all level 3 region files and event file are already downloaded into same directory, the region_dir
args = parser.parse_args()
region_dir = sanitize_filename(args.region_dir)
log = get_logger("create_regions_db")
with work_within_directory.work_within_directory(region_dir):
# Find all region files
region_files = find_files.find_files('.', '*_reg3.fits.gz')
log.info("Found %s region files" % len(region_files))
db = collections.OrderedDict()
for i, region_file in enumerate(region_files):
sys.stderr.write("\r%s out of %s" % (i + 1, len(region_files)))
header = fitsio.read_header(region_file, "SRCREG")
parser = argparse.ArgumentParser(description='Create source database')
parser.add_argument('--region_dir', help="Directory containing the regions file for this obsid",
type=str, required=True)
parser.add_argument('--outfile', help="Name of the output (filtered) event file", type=str, required=True)
parser.add_argument("--debug", help="Debug mode (yes or no)", type=bool, required=False, default=False)
# assumption = all level 3 region files and event file are already downloaded into same directory, the region_dir
args = parser.parse_args()
region_dir = sanitize_filename(args.region_dir)
log = get_logger("create_regions_db")
with work_within_directory.work_within_directory(region_dir):
# Find all region files
region_files = find_files.find_files('.', '*_reg3.fits.gz')
log.info("Found %s region files" % len(region_files))
db = collections.OrderedDict()
for i, region_file in enumerate(region_files):
sys.stderr.write("\r%s out of %s" % (i + 1, len(region_files)))
header = fitsio.read_header(region_file, "SRCREG")
import os
import subprocess
import astropy.io.fits as pyfits
from chandra_suli.run_command import CommandRunner
from chandra_suli.logging_system import get_logger
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Create new event files separated by CCD')
parser.add_argument('--evtfile', help="Event file name", type=str, required=True)
args = parser.parse_args()
logger = get_logger("separate_CCD.py")
runner = CommandRunner(logger)
print "Separating by CCD..."
for ccd_id in range(10):
ccd_file = "ccd_%s_%s" % (ccd_id, os.path.basename(args.evtfile))
cmd_line = "dmcopy %s[EVENTS][ccd_id=%s] %s clobber=yes" % (args.evtfile, ccd_id, ccd_file)
runner.run(cmd_line)
# check if certain CCD files are empty and then delete them if so
f = pyfits.open("%s" % (ccd_file))
